I think what Conrad is saying is that it should work exactly how you're expecting it to work i.e. you can change the setting to shutdown the PC when the profiles finish... but that would be a temporary setting - only valid for the currently running profiles - and it would default back to not shutting down the PC next time. That's certainly how it works for me with SyncbackSE.
Are you absolutely sure it's Syncback causing the shutdown?
Are you absolutely sure it's Syncback causing the shutdown?